CRISPR-Cas9 is a bacterial adaptive immune system that emerged as the centerpiece of a transformative genome editing technology. In this system, an intriguing allosteric communication has been suggested to control the DNA cleavage activity through the flexibility of the catalytic HNH domain. Here, we report about the use of molecular dynamics and graph theory-based analysis methods to describe the structural and dynamic determinants of the allosteric signaling in the CRISPR-Cas9 complex. Network models derived from graph theory reveal the existence of a contiguous dynamic pathway that enables the information transfer across the HNH domain. This pathway spans HNH from the region interfacing the RuvC nuclease and propagates up to the DNA recognition lobe in the full-length CRISPR-Cas9, such transferring the signal of DNA binding at the nuclease domains for concerted cleavages of the two DNA strands. These findings reveal the mechanism of signal transduction within the CRISPR-Cas9 nuclease and pose the basis for the complete mapping of the allosteric pathway, and of its role in the DNA on-target specificity, helping engineering efforts aimed at improving the genome editing capability of CRISPR-Cas9.

Harnessing graph theory to decrypt the allosteric mecahnism in CRISPR-Cas9

ACS Spring Meeting 2021

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